Hey folks, prepare for a long winded and pretty detailed explanation of what's happening to my truck here. Trying to figure this out and need a couple more experienced opinions.

So I have a very awkward vibration happening with my 99 Ram. Has a 5.2 Magnum motor with close to 169k miles on it. Feels like it has a ghost misfire.

What happens:
First start on a cold morning, whistles through the intake and the truck has a shake to it. You open the hood and you can see the motor shaking like it has a misfire, but there are no misfire CEL's occuring. Now I've attributed the whistle to the Idle Air Control as the truck makes the same noise when I pour some Seafoam down the throttle body as well as the noise dissipating completely when the truck has warmed up and idle settles down.

Now to the shake. It's felt through the entire truck and it's more prevalent when the truck is cold. As the truck warms up, you feel the vibration less and less. When the truck gets fully heated, you can't feel the vibration at idle, but you can see the RPMs on the tach jumping about 200 - 300 rpm and you can feel a bit like it misfires. When I accelerate you can feel the vibration shake the truck and it goes away a bit when it hits about 1500rpm. It really depends on how I accelerate. If I would accelerate quickly, the vibration isn't felt and the truck pulls very hard.

Regardless of whether or not the truck is in park/neutral, drive, reverse, or in 4x4, the vibration is still there. When I rev the truck in park/neutral, the you can feel the vibration. Same goes for in drive. Again, it feels like its a misfire, but there are no codes.

What has been done
- Rebuilt trans 3k miles ago - The PO did this to the truck, I have receipts and all. I got the truck in trade and aside from driving around perfectly, this vibration is all that has been bothering me.
- New Cap, rotor, spark plugs, plug wires
- 2x seafoam treatments - truck burns off a lot of white smoke mixed with blue (oil) smoke after a couple minutes of running with the seafoam. My guess is the oil being burned is residue after years of driving? My Datsun did the same thing and stopped after I Seafoamed the hell out of it.
- Cat converter has been hollowed out - I did this as more of a preventative measure. I heard of these trucks clogging their cats and since I have no emissions, I only did what was natural and gutted the cat. I DO have a CEL for my after cat O2 sensor though. This can be remedied by a defouler to move the sensor further away from the exhaust.

As for some random things that occur, if I drive through a puddle on my passenger side (or get anything considerably wet for that matter, only on that side) my truck will try to bog down and will backfire like it lost spark. The only way to get the truck from bogging out is to go full throttle. Then it picks itself up and goes. At that point, I still have no other CEL's other than my after cat O2 sensor, and that only came up after I gutted the cat.

So, any ideas gents? I do all of my own work, so no need to bring it to a shop, just lay it on me.